I run a particular /r/ with a couple hundred thousand subscribers. What I would like to do is to be able to limit brigading. I havea controversial idea on how to do this: If you a subscriber to /r/X then you may not subscribe and vote in /r/Y. IF you're posting in /r/X you may not post in /r/Y
This would then turn shenanigans into private subs... but at least it would be a start.
I could swear /r/4chan had a no raiding other subreddits rule, but I checked and it does not as of right now, that I could find.
Some sort of "honor code between mods" could enforce that quite well. Be a jerk in /r/Y and get kicked out of /r/Y AND /r/X. Be a jerk in any sports subreddit and get tossed out of all of them. Some form of "shared blacklist" cross linked between subreddits could implement this. Assuming the source of the problem is just the users and not one of the mods themselves.
This would then turn shenanigans into private subs... but at least it would be a start.